An atomic-scale ripple structure has been revealed by electron tomography based on sequential projected atomicresolution images, but it requires harsh imaging conditions with negligible structure evolution of the imaged samples. Here, we demonstrate that the ripple structure in monolayer MoSe 2 can be facilely reconstructed from a single-frame scanning transmission electron microscopy (STEM) image collected at designated collection angles. The intensity and shape of each Se 2 atomic column in the single-frame projected STEM image are synergistically combined to precisely map the slight misalignments of two Se atoms induced by rippling, which is then converted to threedimensional (3D) ripple distortions. The dynamics of 3D ripple deformation can thus be directly visualized at the atomic scale by sequential STEM imaging. In addition, the reconstructed images provide the first opportunity for directly testing the validity of the classical theory of thermal fluctuations. Our method paves the way for a 3D reconstruction of a dynamical process in twodimensional materials with a reasonable temporal resolution.